Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential

Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.

Draft Genome Sequences of Enterococcus faecium, Enterococcus gallinarum, and Lactococcus lactis Strains Isolated from a Mastitis-Infected Camel in Isiolo County, Kenya

We report the draft genome sequences and annotation of Enterococcus faecium, Enterococcus gallinarum, and Lactococcus lactis isolates that were recovered from a mastitis-infected camel in Isiolo County, Kenya. Collectively, these data provide an invaluable repository for data mining to support the development of a potential multicomponent mastitis subunit vaccine.

A comparative study of antagonistic activity spectra of lactic acid bacteria isolated from fermented foods

The present work aimed to assess the general antagonistic activity against opportunistic pathogens and to compare antagonistic action spectra of lactic acid bacteria (LAB) strains, isolated from Ukrainian traditional fermented foods. Overall, 161 profiles of the antagonistic activity spectrum were obtained from 1056 LAB strains. Among them, 114 profiles were genus-specific and 47 spectra of antagonistic activity were found in LAB strains of different genera. Furthermore, 19 LAB strains were active only against Gram-negative indicator strains and 149 LAB strains only against Gram-positive indicator strains. The size of growth inhibition zones of indicator strains by LAB strains of each genus did not correlate with the level of acidification. Zones of growth inhibition of indicator strains appeared after 6-8 h of incubation and in most cases decreased with further incubation, up to absence after 24 h. The difference in the antagonistic activity of 16-h-old and 24-h-old hours LAB cultures also was found. Among LAB tested, 241 strains are the most promising for further practical use, they have antagonistic action towards 10 indicator strains. The cross-streaking method can be used for rapid screening of bacteriocinogenic LAB strains and has advantages over the well-diffusion assay. To the best of our knowledge, this is the first report on a comparative characteristic of spectra of antagonistic activity against opportunistic pathogens of LAB strains belonging to different genera.

Antiviral Activity of Exopolysaccharides Produced by Lactic Acid Bacteria of the Genera Pediococcus, Leuconostoc and Lactobacillus against Human Adenovirus Type 5

Background and objectives: The use of antagonistic probiotic microorganisms and their byproducts represents a promising approach for the treatment of viral diseases. In the current work, the effect of exopolysaccharides (EPSs) produced by lactic acid bacteria from different genera on the structural and functional characteristics of cells and the development of adenoviral infection in vitro was studied. Materials and Methods: Cytotoxicity of six EPSs of lactic acid bacteria of the genera Lactobacillus, Leuconostoc and Pediococcus was determined by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. The influence of the EPSs on the infectivity of human adenovirus type 5 (HAdV-5) and on the cell cycle under a condition of adenovirus infection was studied using plaque reduction assay and flow cytometric analysis, respectively. Results: It was shown that exopolysaccharides were non-toxic to Madin-Darby bovine kidney cells (MDBK) as they reduced their viability by 3-17%. A change in the distribution of the cell cycle phases in the non-infected cell population treated with EPSs was observed. The analysis demonstrated an increase in the number of cells in the S phase by 47% when using EPSs 15a and a decrease in the number of cells in the G1 phase by 20-27% when treated with the EPSs 15a, 33a, and 19s. The use of EPSs did not led to the normalization of the life cycle of HAdV-5 infected cells to the level of non-infected cells. The EPSs showed low virucidal activity and reduced the HAdV-5 infectivity to 85%. Among the studied exopolysaccharides, anti-adenovirus activity was found for EPS 26a that is produced by Lactobacillus spp. strain. The treatment of cells with the EPS following virus adsorption completely (100%) suppressed the formation and release of HAdV-5 infectious. Conclusions: EPS 26a possessed distinct anti-HAdV-5 activity and the obtained data demonstrate the potential of using exopolysaccharides as anti-adenoviral agents.